• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.1
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• pp.1-6
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• 2000

For the rapid selection of higher recombinant hirudin producing strain in a methylotrophic yeast Hansenula polymorpha, a multiple gene integration and dose-dependent selection vector, based on a telomere-associated ARS and a bacterial aminoglycoside 3-phosphotransferase (aph) gene, was adopted. Two hirudin expression cassettes (HV1 and HV2) were constructed using the MOX promoter of H. polymorpha and the mating factor $\alpha$ secretion signal of S. cerevisiae. Multiple integrants of a transforming vector containing hirudin expression cassettes were easily selected by using an antibiotic, G418. Hirudin expression level and integrated plasmid copy number of the tested transformants increased with increasing the concentration of G418 used for selection. The expression level of HV1 was consistently higher than that of HV2 under the similar conditions, suggesting that the gene context might be quite important for the high-level gene expression in H. polymorpha. The highest hirudin producing strain selected in this study produced over 96 mg/L of biologically active hirudin in a 500-mL flask and 165 mg/L in a 5-L fermentor.

• Journal of Microbiology and Biotechnology
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• v.24 no.11
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• pp.1503-1509
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• 2014

With the purpose of facilitating the process of stable strain generation, a shuttle vector for integration of genes via a double recombination event into two ectopic sites on the Sulfolobus acidocaldarius chromosome was constructed. The novel chromosomal integration and expression vector pINEX contains a pyrE gene from S. solfataricus P2 ($pyrE_{sso}$) as an auxotrophic selection marker, a multiple cloning site with histidine tag, the internal sequences of malE and malG for homologous recombination, and the entire region of pGEM-T vector, except for the multiple cloning region, for propagation in E. coli. For stable expression of the target gene, an ${\alpha}$-glucosidase-producing strain of S. acidocaldarius was generated employing this vector. The malA gene (saci_1160) encoding an ${\alpha}$-glucosidase from S. acidocaldarius fused with the glutamate dehydrogenase ($gdhA_{saci}$) promoter and leader sequence was ligated to pINEX to generate pINEX_malA. Using the "pop-in" and "pop-out" method, the malA gene was inserted into the genome of MR31 and correct insertion was verified by colony PCR and sequencing. This strain was grown in YT medium without uracil and purified by His-tag affinity chromatography. The ${\alpha}$-glucosidase activity was confirmed by the hydrolysis of $pNP{\alpha}G$. The pINEX vector should be applicable in delineating gene functions in this organism.

• Journal of fish pathology
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• v.22 no.3
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• pp.375-382
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• 2009

Integration and expression of a target gene into chromosomal genomes of host cell by retrovirus mediated gene transfer system usually require complicate and laborious procedures. In the present study, we investigate a simple method to integrate a target gene into genome of BF-2 cells using ultraviolet (UV)-inactivated snakehead retrovirus (SnRV), a fish retrovirus. First of all, an optimization of transfection condition was determined with BF-2 cells using Lipofectamine 2000 and Transome. Using 0.5 $\mu\ell$ Lipofectamine 2000 resulted in 33.8, 40.6 and 40.2% of transfection efficacy with high survival rate (minimum 80%) in 0.5, 1 and 2 $\mu{g}$ DNA, respectively, and those of Transome were all less than 5%. It was confirmed that UV-treatment for 5 min was enough to inactivate infectivity of SnRV. Next, a cassette composed of GFP (green fluorescent protein) gene flanked by LTR (long terminal repeats) sequences derived from SnRV was constructed and transfected into BF-2 cells followed by treatment with UV-inactivated SnRV for optimization of integration and expression of the cassette gene. As the results, the fluorescence was expressed in BF-2 cells treated with UV-inactivated SnRV 3 and 5 times, while there was no expression in BF-2 cells with once and non treatment. Accordingly, it was confirmed that GFP gene was integrated into chromosomal genome of BF-2 cells with UV-inactivated SnRV.

• Journal of Microbiology and Biotechnology
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• v.16 no.6
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• pp.979-982
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• 2006

Two knockout vectors, in which the truncated Kluyveromyces lactis URAS gene is flanked by a direct repeat, were developed for Saccharomyces cerevisiae. Each vector was designed to harbor 5'- and 3'-end homology regions for integration. Two knockout fragments were devised to integrate into the correct locus in a complementary manner to disrupt a gene of interest and. concomitantly to make functional Kl URA3 for transfomant selection. The use of dual complementary knockout cassettes was expected to dramatically reduce integration into unwanted loci in the genome. The knockout system developed in this study was successfully used for disruption of the GAL1 gene in S. cerevisiae.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.53-55
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• 2000

Xenie is the JAVA application software that integrates and represents 'gene to function'information of human gene. Xenie extracts data from several heterogeneous molecular biology databases and provides integrated information in human readable and machine usable way. We defined 7 semantic frame classes (Gene, Transcript, Polypeptide, Protein_complex, Isotype, Functional_object, and Cell) as a common schema for storing and integrating gene to function information and relationship. Each of 7 semantic frame classes has data fields that are supposed to store biological data like gene symbol, disease information, cofactors, and inhibitors, etc. By using these semantic classes, Xenie can show how many transcripts and polypeptide has been known and what the function of gene products is in General. In detail, Xenie provides functional information of given human gene in the fields of semantic objects that are storing integrated data from several databases (Brenda, GDB, Genecards, HGMD, HUGO, LocusLink, OMIM, PIR, and SWISS-PROT). Although Xenie provide fully readable form of XML document for human researchers, the main goal of Xenie system is providing integrated data for other bioinformatic application softwares. Technically, Xenie provides two kinds of output format. One is JAVA persistent object, the other is XML document, both of them have been known as the most favorite solution for data exchange. Additionally, UML designs of Xenie and DTD for 7 semantic frame classes are available for easy data binding to other bioinformatic application systems. Hopefully, Xenie's output can provide more detailed and integrated information in several bioinformatic systems like Gene chip, 2D gel, biopathway related systems. Furthermore, through data integration, Xenie can also make a way for other bioiformatic systems to ask 'function based query'that was originally impossible to be answered because of separatly stored data in heterogeneous databases.

• Horticultural Science & Technology
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• v.30 no.6
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• pp.734-742
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• 2012

To compare RNA interference-mediated gene silencing technique and T-DNA integration for gene function analysis in Chinese cabbage, BrSAMS-knockout (KO) line and BrSAMS-knockdown (KD) line were used. The KO line had lost the function of a Brassica rapa S-adenosylmethionine synthetase (BrSAMS) gene by T-DNA insertion and the KD line had shown down-regulated BrSAMS genes' expression by dsRNA cleavage. From microarray results of the KO and KD lines, genes linked to SAMS such as sterol, sucrose, homogalacturonan biosynthesis and glutaredoxin-related protein, serine/threonine protein kinase, and gibberellin-responsive protein showed distinct differences in their expression levels. Even though one BrSAMS gene in the KO line was broken by T-DNA insertion, gene expression pattern of that line did not show remarkable differences compared to wild type control. However, the KD line obtained by RNAi technique showed prominent difference in its gene expression. Besides, change of polyamine and ethylene synthesis genes directly associated with BrSAMS was displayed much more in the KD line. In the microarray analysis of the KO line, BrSAMS function could not be clearly defined because of BrSAMS redundancy due to the genome triplication events in Brassicaceae. In conclusion, we supposed that gene knock-down method by RNAi silencing is more effective than knock-out method by T-DNA insertion for gene function analysis of polyploidy crops such as Chinese cabbage.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.6
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• pp.523-527
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• 2004

Recombinant Saccharomyces cerevisiae expression systems were developed to pro­duce a novel human anti-angiogenic protein called LK8, an 86 amino-acid kringle fragment pro­tein with three disulfide linkages. Galactose-inducible LK8 expression plasmid was constructed, and LK8 production levels by four S. cerevisiae strains were compared in order to select an op­timal host strain. S. cerevisiae 2805 was the most efficient among the strains tested. Elevating the LK8 gene copy number through multiple integration using 8-sequences as target sites re­sulted in more than a two-fold increase in the LK8 production level compared with the plasmid­based expression system. The maximum LK8 protein concentration of 25 mg/L was obtained from batch cultivation of the yeast transformant that harbors 16 copies of the LK8 gene. In con­clusion, the strain integrated with the multiple LK8 gene secreted the protein with relatively high yield, although, the increased LK8 gene dosage over 11 copies did not lead to further en­hancement in batch cultivations.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.10
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• pp.1367-1372
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• 2000

The present study was conducted to evaluate the efficiency of transgenic rabbit production by DNA microinjection using EGFP (Enhanced Green Fluorescent Protein) gene. In this experiment EGFP coding sequences fused to CMV promoter were microinjected into rabbit one-cell embryos, and then GFP expression and gene integration were evaluated in preimplantation embryos and fetuses recovered on day 15 of pregnancy to determine efficiency of transgenic rabbit production. Effect of DNA concentration was also tested on development in vitro following microinjection and transgene integration in fetuses. Development of embryos in vitro was decreased by DNA microinjection, but the rates of pregnancy and implantation were not significantly affected by microinjection. As development progressed in vitro percentage of GFP expression in rabbit embryos was decreased, resulting GFP expression detected in 37.5% of blastocysts. The efficiencies for production of transgenic fetuses were 4.0% and 7.6%, respectively, when $10ng/{\mu}l$ and $20ng/{\mu}l$ of DNA concentration were microinjected. Transgenic fetuses were confirmed by GFP expression and PCR analysis of fetus genomic DNA. These results indicated that DNA microinjection itself damaged embryo development and DNA concentration affected the efficiency of transgenic rabbit production.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2869-2873
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• 2014

Background: Human papillomavirus (HPV) integration within the E2 gene has been proposed as a critical event in cervical carcinogenesis. This study concerned whether HPV16 status and E2 gene intactness are predictive of radiation response in patients with cervical cancer. Materials and Methods: Biopsies of 44 patients with cervical cancer were collected before or after radiotherapy. The presence of HPV16 was assessed by polymerase chain reaction (PCR) using specific primers for the L1 region. E2 disruption was detected by amplifying the entire E2 gene. Results: HPV16 DNA was found in 54.5% of the clinical samples. Overall, 62.5% of the HPV16 positive tumors had integrated viral genome and 37.5% had episomal genome. There was a tendency of increase of HPV16 E2 negative tumors compared with HPV16 L1 ones in advanced stages (75% versus 20% in stage III respectively). Detection of E2 gene appeared influenced by the radiotherapy treatment, as the percentage of samples containing an intact HPV16 E2 was more frequent in pretreated patients compared to radiotherapy treated patients (66.6% versus 20%). The radiation therapy caused an eight-fold [OR= 8; CI=1.22-52.25; p=0.03] increase in the risk of HPV16 genome disruption. The integration status is influenced by the irradiation modalities, interestingly E2 disruption being found widely after radiotherapy treatment (75%) with a total fractioned dose of 50Gy. Conclusions: This study reveals that the status of the viral DNA may be used as a marker to optimize the radiation treatment.

• Microbiology and Biotechnology Letters
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• v.23 no.5
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• pp.544-549
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• 1995

The alkaline elastase is an extracellular serine protease of the alkalophilic Bacillus strain Ya-B. To increase the gene copy number and the production level of the alkaline elastase Ya-B, we designed, on the B. subtilis chromosome, a gene amplification of the 10.6 kb repeating unit containing amyE, aleE (alkaline elastase Ya-B gene) and tmrB. The aleE was inserted between amyE and tmrB, and B. subtilis APT119 strain was transformed with this amyE-aleE-tmrB-junction region fragment. As a result, we succeeded in obtaining tunicamycin-resistant (Tm$^{r}$) transformants (Tf-1, Tf-2) in which the designed gene amplification of 10.6 kb occurred in chromosome. The transformants showed high productivity of $\alpha $-amylase and alkaline elastase Ya-B. The copy number of the repeating unit (amyE-aleE-tmrB) was estimated to be 25, but plasmid vector (pUC19) was not integrated. The amplified aleE of chromosome was more stable than that of plasmid in absence of antibiotics.